Updated srwl_bl.py and srwlib.py added to allow correct import in Sirepo #7

mrakitin · 2016-03-02T17:29:19Z

Dear Oleg,

Please revise the suggested changes to your code, which will allow better integration with Sirepo.

Thanks,
Maksim

…epo.

…y) added.

…y.so copied from rs/SRW-light.

… are ignored now.

…nd core+pylib (make).

ochubar · 2016-07-31T16:23:01Z

env/work/srw_python/srwlib.py

@@ -342,6 +342,12 @@ def get_K(self):
            sumBdNe2 += curBdN*curBdN
        return mult*self.per*sqrt(sumBdNe2)

+    def K_2_B(self, K):


OK. Implemented fully (added member-function def K_2_B(self, K)).

ochubar · 2017-11-14T22:05:53Z

env/work/srw_python/srwlib.py

@@ -3769,7 +3772,7 @@ def srwl_uti_write_data_cols(_file_path, _cols, _str_sep, _str_head=None, _i_col
        if(nLines < newLen): nLines = newLen

    strSep = '\t'
-    if(_str_sep != None):
+    if(_str_sep is not None):


OK. "== None" / "!= None" is fixed in all places.

ochubar · 2017-11-14T22:18:20Z

env/work/srw_python/uti_io.py

+        'data': data,
+        'raw_image': raw_image,
+        'limit_value': limit_value,
+    }


OK, done. Updated this.
It's good to see the previous processing (cutting label, etc.) was removed from here. "read_image()" has just read an image from file.

I'm glad you like it. Yes, the simpler this function, the better. All the processing is done in the Sample library.

ochubar · 2017-11-14T22:27:42Z

env/work/srw_python/uti_math.py

+            return {
+                'fwhm': abs(list_of_roots[-1] - list_of_roots[0]),
+                'x_range': list_of_roots,
+            }
    else:
        raise Exception('Number of roots is less than 2!')


OK, done.
BTW, do we really need the "fwhm_scipy(x, y)" function that goes after this one?

It can be removed, it's not used anywhere. The function was originally created by Timur with the scipy dependency.

I removed this function.

ochubar · 2017-11-14T22:39:59Z

env/work/srw_python/uti_plot.py

-    _backend.uti_data_file_plot(_fname, _read_labels, _e, _x, _y, _graphs_joined, _traj_report, _traj_axis) #MR29072016
+    _backend.uti_data_file_plot(_fname, _read_labels, _e, _x, _y, _graphs_joined,
+                                _multicolumn_data, _column_x, _column_y, #MR31102017
+                                _scale, _width_pixels) #MR20012017


ochubar · 2017-11-14T22:47:31Z

env/work/srw_python/uti_plot_com.py

+            'units': units,
+        }
+    # data, mode, allrange, arLabels, arUnits
+    return d, None, [], [], []


OK, I added "_multicolumn_file_load(fname)", but also left the "_traj_file_load(fname, traj_axis='x')" for backwards compatibility. I marked the latter one as OBSOLETE.

ochubar · 2017-11-14T22:51:12Z

env/work/srw_python/uti_plot_com.py

        return _file_load(fname, read_labels)
    else:
-        return _traj_file_load(fname, traj_axis)
+        return _multicolumn_file_load(fname)


ochubar · 2017-11-14T23:01:57Z

env/work/srw_python/uti_plot_matplotlib.py

+                data = np.reshape(data, (data.shape[0] * data.shape[1]), order='C')
+            except:
+                print('Cannot resize the image - scipy.ndimage.zoom() cannot be imported.')
+                pass


OK, updated this; though it is not clear which exactly lines had to be deleted (I made a guess).

I think I only added the code, didn't remove anything in this place since there are only green lines with + symbols, no red color with -.

ochubar · 2017-11-14T23:05:37Z

env/work/srw_python/uti_plot_matplotlib.py

+            for c in [_column_x, _column_y]:
+                if c not in available_cols:
+                    raise ValueError('Incorrect column specified: {}.\nAvailable columns: {}'.format(c, available_cols))
+            fig = self._plot_1D_XvsY(data, _column_x, _column_y)


OK, added this.

ochubar · 2017-11-14T23:06:43Z

env/work/srw_python/uti_plot_matplotlib.py

+        ax.grid()
+        ax.set_xlabel(data[column_x]['label'])
+        ax.set_ylabel(data[column_y]['label'])
+        return fig


OK, added this.

ochubar · 2017-11-16T16:58:56Z

env/work/srw_python/uti_plot_matplotlib.py

        return self._maybe_savefig(fig)

    def _enum(self, *sequential, **named): #Had to copy this in uti_plot_com
        enums = dict(zip(sequential, range(len(sequential))), **named)
        return type('Enum', (), enums)

+    def _plot_1D_XvsY(self, data, column_x, column_y, figsize=(8, 5), typ=111): #MR31102017


Actually, this function would rather be called "_plot_1D_YvsX". But OK, I left it "as is" for the moment.

ochubar · 2017-11-16T17:03:35Z

env/work/srw_python/SRWLIB_ExampleViewDataFile.py


    #print(opt.joined)
    uti_plot_init('TkAgg')
    #uti_data_file_plot(opt.infile, opt.readlab, opt.e, opt.x, opt.y, opt.joined)
-    uti_data_file_plot(opt.infile, opt.readlab, opt.e, opt.x, opt.y, opt.joined, opt.traj_report, opt.traj_axis) #MR29072016
+    uti_data_file_plot(opt.infile, opt.readlab, opt.e, opt.x, opt.y, opt.joined,


All other main functions in this module start from "uti_plot" prefix. So I've changed the name of this main function to "uti_plot_data_file", but also left the "uti_data_file_plot" version for backwards-compatibility.

ochubar · 2017-11-16T17:34:51Z

env/work/srw_python/basic-test.sh

+fi
+
+# Test of multielectron simulation for nan/inf values:
+example_py="multielectron_test.py"


I've modified this file name: "multielectron_test.py" -> "srwl_test_multi_e.py" and made the corresponding correction here.

ochubar · 2017-11-16T17:39:53Z

env/work/srw_python/basic-test.sh

+
+# Test of multielectron simulation for nan/inf values:
+example_py="multielectron_test.py"
+data_d="multielectron_test"


Also, I changed this directory name to "data_test" - to obey general naming conventions used in SRW.

ochubar · 2017-11-16T17:56:05Z

Makefile

-	    cd $(root_dir); \
-	    rm -rf $(example10_data_dir); \
-	fi;
+	timeout_s=$(timeout) bash $(examples_dir)/basic-test.sh


Modified the bash file name here: "basic-test.sh" -> "srwl_test_basic.sh"

ochubar · 2017-11-17T01:19:47Z

env/work/srw_python/srwl_uti_smp.py

+
+    opT.input_parms = input_parms
+
+    return opT


OK, I took the entire file (without testing).

I've tested it with Sirepo yesterday, seems to work fine.

ochubar · 2017-11-17T15:46:03Z

env/work/srw_python/uti_plot_matplotlib.py

+        if not _multicolumn_data:
+            data = np.array(data)
+        if mode == 3:
+            try:


Why "mode == 3"? It may have values of _enum('T','V','H','E','HV','EV','EH','EHV')
We don't seem to need FWHM printed here. E.g. it is confusing in the case of spectrum over photon energy.
I commented this part out.

mode=3 was for E, just convenience I used for myself. It's fine it's commented out for me.

ochubar · 2017-11-17T22:11:21Z

env/work/srw_python/uti_math.py


    def is_positive(num):
        return True if num > 0 else False

+    # Normalize values first:
+    y = (y - min(y)) / (max(y) - min(y)) - shift  # roots are at Y=0


Maksim, this doesn't seem to work with Python native array.array()...
This is what I get when trying to execute SRWLIB_Example15.py:
Traceback (most recent call last):
File "C:\SoftwareDevelopments\SRW_Dev\env\work\srw_python\SRWLIB_Example15.py", line 191, in
xRMS.append(fwhm(x, arIxh))
File "C:\SoftwareDevelopments\SRW_Dev\env\work\srw_python\uti_math.py", line 636, in fwhm
y = (y - min(y)) / (max(y) - min(y)) - shift # roots are at Y=0
TypeError: unsupported operand type(s) for -: 'list' and 'float'

If you are busy, I'll fix this myself. I want to update SRW on GitHub today or tomorrow.

Fixed in 0aa2404.

(ochubar#7 (comment))

(ochubar/SRW#7 (comment))

mrakitin · 2017-11-21T04:24:05Z

I synchronized the changes with my repo, there is no difference in files, closing the pull request (PR). In the future I'll be submitting each PR from a separate branch to allow easier and automatic synchronization.

mrakitin and others added 8 commits March 2, 2016 17:25

Updated srwl_bl.py and srwlib.py added to allow correct import in Sir…

1892902

…epo.

Improvements for support of arbitrary input arguments in srwl_bl.py.

ff0fecf

Improvements for arguments parsing.

8fb3a49

Simplify naming of arguments and their processing.

b4023e1

Crystal element object updated to allow import in Sirepo.

838b629

Type of 2D mirror profile corrected.

b52330c

Compiling script for srwlpy.so added.

45dd006

Compiling script for srwlpy.so added.

208e9cc

mrakitin force-pushed the master branch from 208e9cc to 45dd006 Compare March 25, 2016 04:43

mrakitin and others added 14 commits March 25, 2016 00:44

Merge branch 'master' of https://github.com/mrakitin/SRW

9b42e34

SRW examples 15 (GaussianBeamPropagation.py) and 16 (GaussBeamDiffr.p…

9b9e1a7

…y) added.

compile.sh updated to download fftw archive if it is not found. srwlp…

307c532

…y.so copied from rs/SRW-light.

Fixed incorrect False usage in uti_plot_matplotlib.py. The .pyc files…

61432f8

… are ignored now.

Makefile updated to allow compilation of fftw+core+pylib (make all) a…

4954d4f

…nd core+pylib (make).

Makefile updated with test and adapted for light SRW version.

13f63a5

Remove compile.sh since its functionality implemented in Makefile.

1b1533e

Sync with SRW-light.

846409d

Fix of Makefile for POSIX sh.

afca8ab

Description added to Makefile.

320501b

K to B converter added to implement sirepo/#9 later.

b46cdc0

Sync with radiasoft/SRW-light.

1028afc

Trajectory report plotting enabled.

9b75d64

Changes from Oleg in Example 15.

ddeac6e

ochubar reviewed Jul 31, 2016
View reviewed changes

ochubar reviewed Nov 14, 2017

View reviewed changes

ochubar reviewed Nov 16, 2017

View reviewed changes

mrakitin added 2 commits November 16, 2017 15:06

Added try/except check for missing libraries inside the method.

c713c7a

Remove unused FWHM function with SciPy calls.

fd69664

ochubar reviewed Nov 17, 2017

View reviewed changes

mrakitin mentioned this pull request Nov 17, 2017

Improve SRW tests radiasoft/SRW-light#5

Closed

ochubar reviewed Nov 17, 2017

View reviewed changes

BUG: FWHM calculation fix for native lists

0aa2404

(ochubar#7 (comment))

mrakitin added a commit to radiasoft/SRW-light that referenced this pull request Nov 18, 2017

BUG: FWHM calculation fix for native lists

ffb21c7

(ochubar/SRW#7 (comment))

mrakitin added 5 commits November 20, 2017 23:01

Synch with 6af0424

23cc233

Merge remote-tracking branch 'upstream/master'

6bbe727

Remove versioned .pyd files to sync with ochubar/SRW.

4970fd3

.gitignore synch

83cef92

Removed basic-test.sh and multielectron_test.py.

f8a2e6f

mrakitin closed this Nov 21, 2017

mrakitin mentioned this pull request Mar 4, 2022

Update SRW project structure #37

Closed

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Updated srwl_bl.py and srwlib.py added to allow correct import in Sirepo #7

Updated srwl_bl.py and srwlib.py added to allow correct import in Sirepo #7

mrakitin commented Mar 2, 2016

ochubar Jul 31, 2016 •

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mrakitin commented Nov 21, 2017

Updated srwl_bl.py and srwlib.py added to allow correct import in Sirepo #7

Updated srwl_bl.py and srwlib.py added to allow correct import in Sirepo #7

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mrakitin commented Mar 2, 2016

ochubar Jul 31, 2016 • edited Loading

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mrakitin commented Nov 21, 2017

ochubar Jul 31, 2016 •

edited

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